Image analysis in R: matching the TIFF image with the corresponding point pattern match
so I'm using spatstat package in R, and analyzing a TIFF segmentation mask image as well as the corresponding planar point pattern (using only the X,Y coordinates of the segmented object centroids).
For clarity, the planar point pattern object contains X,Y coordinates (centroids) of the objects from the TIFF segmentation image. I am trying to plot the X,Y coordinates in a layered manner which shows the mask and the centroids.
However when I load the TIFF image that contains a visual image of the boundary points the window. The dimensions of the TIFF image is 2800X2800
vim integer-valued pixel image 2800 x 2800 pixel array (ny, nx) enclosing rectangle: [0, 2800] x [0, 2800] micrometer
The corresponding point patterns range from (X: 2X700) and Y: (2X700).
types$RB Planar point pattern: 835 points window: rectangle = [2.1364, 699.1579] x [1.5143, 699.3214] units (one unit = 2 micrometer)
How do I align up these two coordinate spaces in R using 'spatmat' or another image analysis package?
How do I align the coordinates of the centroids over the segmentation mask?
I could try to rescale the types$RB object so that it has the same dimensions as the TIFF image, however this does not really look like a match.
Update: For this approach, I think it is required to create a shape file from the TIFF file. and then begin overlaying the centroids (X,Y) coordinates over the shape file derived from a TIFF plot.